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  • C12N15/09—Recombinant DNA-technology
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  • C12P21/00—Preparation of peptides or proteins
  • C12P21/005—Glycopeptides, glycoproteins
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
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  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
  • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
  • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
  • C12N15/8257—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits for the production of primary gene products, e.g. pharmaceutical products, interferon
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  • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
  • C12N9/10—Transferases (2.)
  • C12N9/1048—Glycosyltransferases (2.4)
  • C12N9/1077—Pentosyltransferases (2.4.2)
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  • C12Y204/00—Glycosyltransferases (2.4)
  • C12Y204/02—Pentosyltransferases (2.4.2)
  • C12Y204/02038—Glycoprotein 2-beta-D-xylosyltransferase (2.4.2.38)
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  • C12Y—ENZYMES
  • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
  • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
  • C12Y302/01024—Alpha-mannosidase (3.2.1.24)
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  • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
  • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
  • C12Y302/0105—Alpha-N-acetylglucosaminidase (3.2.1.50)
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  • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
  • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
  • C12Y302/01052—Beta-N-acetylhexosaminidase (3.2.1.52)

Definitions

• the invention relates to polynucleotides coding for a ⁇ l,2-xylo- syltransferase. Furthermore, the invention relates to vectors comprising these polynucleotides, recombinant host cells, plants and insects transfected with the polynucleotides or with DNA derived therefrom, respectively, as well as to glycoproteins produced in these systems.
• Glycoproteins exhibit a variety and complexity of carbohydrate units, the composition and arrangement of the carbohydrates being characteristic of different organisms.
• the oligosaccharide units of the glycoproteins have a number of tasks, e.g. they are important in regulating metabolism, they are involved in transmitting cell-cell interactions, they determine the circulation periods of proteins in circulation, and they are decisive for recognizing epitopes in antigen-antibody reactions.
• the glycosylation of glycoproteins starts in the endoplasmatic reticulum (ER) , where the oligosaccharides are either bound to asparagine side chains by N-glycosidic bonds or to serine or threonine side chains by O-glycosidic bonds.
• the N-bound oligosaccharides contain a common core from a penta-saccharide unit which consists of three mannose and two N-acetyl glucose amine residues.
• the proteins are transported from the ER to the Golgi complex.
• the structure of the N-bound oligosaccharide units of glycoproteins is determined by their conformation and by the composition of the glyco- syl transferases of the Golgi compartments in which they are processed.
• N-glycans mannose-deficient or truncated N-glycans, respectively.
• the ⁇ -mannosyl residues may be further replaced by GlcNAc, to which galactose and fucose are bound so that a structure is prepared which corresponds to the human Lewis a-epitope (Melo et al., 1997, FEBS Lett 415, 186-191; Fitchette-Laine et al . , 1997, Plant J. 12, 1411-1417).
• ⁇ l,2-xylose nor the 0.1,3-bound fucose exist in mammalian glycoproteins. It has been found that the ⁇ l,2-xylose together with ⁇ l,3-fucose plays an important role in the epitope recognition of antibodies which are directed against plant N-bound oli- gosaccharides, and thereby trigger immune reactions in human or animal bodies against these oligosaccharides (Faye et al . , 1993, Anal. Biochem. 209, 104-108).
• the ⁇ l,2-xylose and/or ⁇ l,3-fucose containing N-glycans furthermore seem to be one of the main causes for the wide-spread allergic cross reactivity between various plant and insect allergens and is also termed "cross-reactive carbohydrate determinant" (CCD) . Due to the frequent occurrence of immunological cross reactions, the CCDs moreover mask allergy diagnoses .
• CCD cross-reactive carbohydrate determinant
• 2-xylosyltransferase transfers the D-xylose from UDP-xylose to the beta-linked mannose of plant N-linked oligosaccharides .
• the soybean ⁇ l, 2-xylosyltransferase was isolated and purified in 1997. Only a part of the xylosyltransferase cDNA has been isolated, s. W099/29835 Al; SEQ ID NO 6 and 7), however, the complete cDNA, which codes for the active protein could not be isolated and characterized so far. The reason why the nucleotide sequence has not been identified so far could be major problems in the procedure due to very low abundance of the mRNA which codes for the xylosyltransferase in the organisms, as for example soybeans.
• soybean ⁇ l, 2-xylosyl transferase One problem of the isolated soybean ⁇ l, 2-xylosyl transferase is that its solubility and activity depends on the presence of detergents .
• a further object is the production of large quantities of purified recombinant enzyme in order to allow in vi tro synthesis of homogenous N-glycans or glycoconjugates containing ⁇ l,2-xylose. This will aid the further elucidation of the role of ⁇ l,2-xylose in the immunogenicity and allergenicity of plant glycoproteins.
• the object according to the invention is achieved by a DNA mole cule comprising a sequence according to SEQ ID NO: 8 with an open reading frame from base pair 227 to base pair 1831 or being at least 50% homologous to the above sequence or hybridizing with the above-indicated sequence under stringent conditions, or comprising a sequence which has degenerated to the above DNA sequence due to the genetic code, the sequence coding for a plant protein which has ⁇ l, 2-xylosyltransferase activity or is complementary thereto.
• This complete sequence which has never been described is particularly useful for experiments, analysis and production processes which concern the ⁇ l, 2-xylosyltransferase activity.
• This sequence can be used especially for the inactivation or suppression of the ⁇ l, 2-xylosyltransferase as well as for overexpression and production of the recombinant enzyme.
• A. thaliana xylosyltransferase-cDNA may be on the one hand that the xylosyltransferase-mRNA of A. thaliana is less problematic compared to other plant species, on the other hand the PCR was performed with optimally designed gene-specific primers .
• the open reading frame of the SEQ ID NO: 8 codes for a protein with 534 amino acids and with a theoretical molecular weight of 60.2 kDa, a transmembrane portion presumably being present in the region between Hell and Phe29.
• the calculated pi value of the encoded protein of the sequence according to SEQ ID NO: 9 is 7.52.
• the activity of the plant ⁇ l, 2-xylosyltransferase is detected by a method and measured, the xylosyltransferase being added to a sample containing UDP-xylose and a labelled acceptor (e.g. a gly- copeptide or labelled oligosaccharide) . After the reaction time, the content of bound xylose is measured.
• the activity of the xy- losyltransferase in this case is seen as positive if the activity measurement is higher by at least 10 to 20%, in particular at least 30 to 50%, than the activity measurement of the negative control.
• the structure of the oligosaccharide may additionally be verified by means of HPLC.
• the pairing of two DNA molecules can be changed by selection of the temperature and ionic strength of the sample.
• stringent conditions according to the invention conditions are understood which allow for an exact, stringent, binding.
• the DNA molecules are hybridized in 7% sodium dodecyl sulfate (SDS) , 0.5M NaP04, pH 7.0, ImM EDTA at 50°C, and washed with 1% SDS at 42°C.
• SDS sodium dodecyl sulfate
• Whether sequences have an at least 50% homology to SEQ ID NO: 8 can be determined e.g. by means of the program FastDB of EMBL or SWISSPROT data bank.
• the recombinant enzyme is soluble without detergents (e.g. Triton X-100) , whereas the solubility of the enzyme from soybean depends on the presence of detergents.
• detergents e.g. Triton X-100
• the recombinant enzyme is fully active in the absence of detergents (e.g. Triton X-100) .
• the recombinant enzyme is N-glycosylated, whereas the enzyme from soybean is described to be unglycosylated.
• the enzyme from A. thaliana exhibits full enzymatic activity also as a truncated form lacking the 32 N-terminal amino acids.
• the cDNA sequence coding for the soybean enzyme corresponds only to amino acids (aa) 199 - 469 of the A. thaliana protein, see figure 11.
• the cDNA sequence coding for A. thaliana xylosyltransferase contains two insertions (corresponding to aa 375-382 and aa 425- 429 of the predicted protein sequence) compared to the partial sequence of the soybean enzyme, see figure 11.
• Peptide SEQ ID NO. 1 homologous to aa 411-422 of the A . thaliana enzyme
• Peptide SEQ ID NO. 2 homologous to aa 192-205 of the A. thaliana enzyme
• Peptide SEQ ID NO. 3 homologous to aa 451-477 of the A . thaliana enzyme
• Peptide SEQ ID NO. 4 homologous to aa 191-205 of the A. thaliana enzyme
• Peptide SEQ ID NO. 5 homologous to aa 503-512 of the A. thaliana enzyme (remark: the cDNA sequence listed in
• W099/29835 Al does not contain a coding sequence for peptide 5) .
• the DNA molecule according to the present invention is particularly advantageous since it encodes for an active recombinant enzyme which shows surprisingly advantageous characteristics and effects over the known purified enzyme.
• the sequence of the DNA molecule of the invention encodes a protein with a ⁇ l, 2-xylosyltransferase activity.
• This specific protein is especially useful for analysis, experiments and production methods which relate to the ⁇ l, 2-xylosyltransfe- rase.
• the DNA molecule according to the invention is at least 70%, preferably at least 80%, particularly preferred at least 95%, homologous with the sequence according to SEQ ID NO: 8.
• This sequence codes for a particularly active ⁇ l, 2-xylosyl- transferase.
• the homology preferably is determined with a program which recognizes insertions and deletions and which does not consider these in the homology calculation.
• the DNA molecule comprises 1750 to 1850, in particular 1831, base pairs.
• one of the above- indicated DNA molecules is covalently associated with a detectable marker substance.
• a detectable marker substance any common marker can be used, such as, e.g., fluorescent, luminescent, radioactive markers, biotin, etc.
• reagents are provided which are suitable for the detection, selection and quantitation of corresponding DNA molecules in solid tissue samples (e.g. from plants) or also in liquid samples, by means of hybridizing methods.
• the DNA molecule according to the invention includes a sequence which comprises a deletion, insertion and/or substitution mutation.
• the number of mutant nucleotides is variable and varies from a single one to several deleted, inserted or substituted nucleotides . It is also possible that the reading frame is shifted by the mutation. In such a "knock-out gene" it is merely important that the expression of a ⁇ l, 2-xylosyltransferase is disturbed, and the formation of an active, functional enzyme is prevented. In doing so, the site of the mutation is variable, as long as expression of an enzymatically active protein is prevented.
• the mutation in the catalytic region of the enzyme which is located in the C-terminal region.
• the invention further provides a DNA molecule which codes for a ribozyme which comprises two sequence sections, each of which has a length of at least 10 to 15 base pairs each, which are complementary to sequence sections of an inventive DNA molecule as described above so that the ribozyme complexes and cleaves the mRNA which is transcribed by a natural ⁇ l, 2-xylosyltransferase DNA mo- lecule.
• a DNA molecule which codes for a ribozyme which comprises two sequence sections, each of which has a length of at least 10 to 15 base pairs each, which are complementary to sequence sections of an inventive DNA molecule as described above so that the ribozyme complexes and cleaves the mRNA which is transcribed by a natural ⁇ l, 2-xylosyltransferase DNA mo- lecule.
• the ribozyme will recognize the mRNA of the ⁇ l, 2-xylosyl ransferase by complementary base pairing with the mRNA. Subsequently, the ribozyme will cleave and destroy the RNA in a sequence-specific manner, before the enzyme is translated. After dissociation from the cleaved substrate, the ribozyme will repeatedly hybridize with RNA molecules and act as specific endonuclease. In general, ribozymes may specifically be produced for inactivation of a certain mRNA, even if not the entire DNA sequence which codes for the protein is known. Ribozymes are particularly efficient if the ribosomes move slowly along the mRNA.
• minizymes are efficient particularly for cleaving larger mRNA molecules .
• a minizyme is a hammer head ribozyme which has a short oligonucleotide linker instead of the stem/loop II. Dimer-minizymes are particularly efficient (Kuwabara et al., 1998, Nature Biotechnology, 16; 961-965).
• a further aspect of the invention relates to a biologically functional vector which comprises one of the above-indicated DNA molecules.
• a biologically functional vector which comprises one of the above-indicated DNA molecules.
• an independent vector capable of amplification is necessary, wherein, depending on the host cell, transfection mechanism, task and size of the DNA molecule, a suitable vector can be used. Since a large number of different vectors is known, an enumeration thereof would go beyond the limits of the present application and there fore is done without here, particularly since the vectors are very well known to the skilled artisan (as regards the vectors as well as all the techniques and terms used in this specification which are known to the skilled artisan, cf. also Maniatis) .
• the vector has a small molecule mass and should comprise selectable genes so as to lead to an easily recognizable phenotype in a cell so thus enable an easy selection of vector-containing and vector-free host cells.
• the vector should comprise a strong promoter, as well as an enhancer, gene amplification signals and regulator sequences.
• a replication origin is important for an autonomous replication of the vector. Polyadenylation sites are responsible for correct processing of the mRNA and splice signals for the RNA transcripts. If phages, viruses or virus particles are used as the vectors, packaging signals will control the packaging of the vector DNA. For instance, for transcription in plants, Ti plasmids are suitable, and for transcription in insect cells, baculoviruses, and in insects, respectively, transposons, such as the P element.
• the invention relates to a biologically functional vector comprising a DNA molecule according to one of the above- described embodiments, being inversely orientated with respect to the promoter. If this vector is transfected in a host cell, an "antisense mRNA" will be read which is complementary to the mRNA of the ⁇ l, 2-xylosyltransferase and complexes the latter. This bond will either hinder correct processing, transportation, stability or, by preventing ribosome annealing, it will hinder translation and thus the normal gene expression of the ⁇ l, 2-xylosyltransferase.
• a suitable antisense RNA molecule comprises, e.g., from 50 to 200 nucleotides since many of the known, naturally occurring antisense RNA molecules comprise approximately 100 nucleotides.
• rapidly hybridizing RNA molecules are used.
• the efficiency of antisense RNA molecules which have a size of more than 50 nucleotides will depend on the annealing kinetics in vi tro .
• rapidly annealing antisense RNA molecules exhibit a greater inhibition of protein expression than slowly hybridizing RNA molecules (Wagner et al . , 1994, Annu. Rev. Microbiol., 48:713-742; Rittner et al., 1993, Nucl. Acids Res., 21: 1381- 1387) .
• Such rapidly hybridizing antisense RNA molecules particularly comprise a large number of external bases (free ends and connecting sequences) , a large number of structural subdomains (components) as well as a low degree of loops (Patzel et al. 1998; Nature Biotechnology, 16; 64-68) .
• the hypothetical secondary structures of the antisense RNA molecule may, e.g., be determined by aid of a computer program, according to which a suitable antisense RNA DNA sequence is chosen.
• Different sequence regions of the DNA molecule may be inserted into the vector.
• One possibility consists, e.g., in inserting into the vector only that part which is responsible for ribosome annealing. Blocking in this region of the mRNA will suffice to stop the entire translation. A particularly high efficiency of the antisense molecules also results for the 5'- and 3 '-non translated regions of the gene.
• the invention also relates to a biologically functional vector which comprises one of the two last-mentioned DNA molecules (mutation or ribozyme-DNA molecule) . What has been said above regarding vectors also applies in this instance.
• RNA is isolated from a plant cell, in particular from leaf cells, by means of which a reverse transcription is carried out after the addition of a reverse transcriptase and primers.
• the individual steps of this method are carried out according to protocols known per se.
• For the reverse transcription on the one hand, it is possible to produce the cDNA of the entire mRNA with the help of oligo(dT) primers, and only then to carry out a PCR by means of selected primers so as to prepare DNA molecules comprising the ⁇ l, 2-xylosyltransferase gene.
• the selected primers may directly be used for the reverse transcription so as to obtain short, specific cDNA.
• the suitable primers may be prepared e.g. synthetically according to the pattern of cDNA sequences of the transferase.
• the invention furthermore relates to a method of cloning a ⁇ l,2- xylosyltransferase, characterized in that the DNA molecule of the invention is cloned into a vector which subsequently is transfec- ted into a host cell or host, respectively, wherein, by selection and amplification of transfected host cells, cell lines are obtained which express the active ⁇ l, 2-xylosyltransferase.
• the DNA molecule is inserted into the vector by aid of restriction endo- nucleases, e.g..
• restriction endo- nucleases e.g.
• What is important in this method is that an efficient host-vector system is chosen.
• eukaryotic host cells are particularly suitable.
• One possible way is to transfect the vector in insect cells. In doing so, in particular an insect virus would have to be used as vector, such as, e.g., baculovirus .
• plants or plant cells, human or other vertebrate cells can also be transfected, in which case the latter would express an enzyme foreign to them.
• a method of preparing recombinant host cells, in particular plant cells or plants, respectively, with a suppressed or completely stopped ⁇ l, 2-xylosyltransferase production is provided, which is characterized in that at least one of the vectors according to the invention, i.e. that one comprising the inventive DNA molecule, the mutant DNA molecule or the DNA molecule coding for ribozymes or the one comprising the DNA molecule in inverse orientation to the promoter, is inserted into the host cell or plant, respectively. What has been said above for the transfection also is applicable in this case.
• plant cells may, e.g., be used, wherein, e.g., the Ti plasmid with the agrobacterium system is eligible.
• agrobacterium system it is possible to transfect a plant directly: agrobacteria cause root stem galls in plants. If agrobac- teria infect an injured plant, the bacteria themselves do not get into the plant, but they insert the recombinant DNA portion, the so-called T-DNA, from the annular, extrachromosomal, tumour-inducing Ti-plasmid into the plant cells .
• the T-DNA, and thus also the DNA molecule inserted therein, are installed in the chromosomal DNA of the cell in a stable manner so that the genes of the T-DNA will be expressed in the plant.
• the transfected cells are selected, e.g. on the basis of antibiotic resistences for which the vector comprises genes, or other marker genes.
• the transfected cell lines are amplified, either in small amounts, e.g. in Petri dishes, or in large amounts, e.g. in fermentors .
• plants have a particular characteristic, i.e. they are capable to re-develop from one (transfected) cell or from a protoplast, respectively, to a complete plant which can be grown.
• the mutant DNA molecule will recognize the identical sequence in the genome of the host cell despite its mutation and will be inserted exactly on that place so that a "knock-out gene" is formed.
• a mutation is intro- pokerd into the gene for the ⁇ l, 2-xylosyltransferase which is capable of inhibiting the faultless expression of the ⁇ l, 2-xylosyl transferase.
• the gene may be sequenced as an additional check so as to determine the success of the homologous recombination or the degree of mutation, respectively.
• the active ribozyme will be expressed in the host cell .
• the ribozyme complexes the complementary mRNA sequence of the ⁇ l, 2-xylosyltransferase at least at a certain site, cleaves this site, and in this manner it can inhibit the translation of the enzyme.
• ⁇ l, 2-xylosyl- transferase will not be expressed.
• a sense or antisense-mRNA will be expressed in the transfected cell (or plant, respectively) .
• the antisense mRNA is complementary at least to a part of the mRNA sequence of the ⁇ l, 2-xylosyltransferase and may likewise inhibit translation of the enzyme.
• a method of suppressing the expression of a gene by antisense technique reference is made to the publication by Smith et al . , 1990, Mol . Gen. Genet. 224:477-481, wherein in this publication the expression of a gene involved in the maturing process of tomatoes is inhibited.
• Double-stranded RNA has recently been shown to trigger sequence-specific gene silencing in a wide variety of organisms, including nematodes, plants, trypanosomes , fruit flies and planaria; an as yet uncharacterized RNA trigger has been shwon to induce DNA methylation in several different plant systems leading to selective interference with gene function (for review see Fire A., 1999, Trends Genet 15 (9): 358-363).
• ⁇ l, 2-xylosyltransferase is at least suppressed, preferably even completely blocked.
• the degree of the disturbance of the gene expression will depend on the degree of complexing, homologous recombination, on possible sub- sequent coincidental mutations and on other processes in the region of the genome.
• the transfected cells are checked for ⁇ l,2- xylosyltransferase activity and selected.
• Xylo- sylation may be reduced by the action of other mammalian enzymes, the combination of the inhibition of the expression of an active ⁇ l, 2-xylosyltransferase by means of the inventive vector and by means of a mammalian enzyme vector being particularly efficient.
• Any type of plant may be used for transfection, e.g. mung bean, tobacco plant, tomato and/or potato plant.
• Another advantageous method of producing recombinant host cells, in particular plant cells, or plants, respectively, consists in that the DNA molecule comprising the mutation is inserted into the genome of the host cell, or plant, respectively, in the place of the non-mutated homologous sequence (Schaefer et al., 1997, Plant J.,- 11(6) .1195-1206) .
• This method thus does not function with a vector, but with a pure DNA molecule.
• the DNA molecule is inserted into the host e.g. by gene bombardment, microinjection or electroporation, to mention just three examples.
• the DNA molecule binds to the homologous sequence in the genome of the host so that a homologous recombination and thus reception of the deletion, insertion or substitution mutation, respectively, will result in the genome: Expression of the ⁇ l, 2-xylosyltransferase can be suppressed or completely blocked, respectively.
• recombinant plants or plant cells are provided which have been prepared by one of the methods described above, their ⁇ l, 2-xylosyltransferase production being suppressed or completely blocked, respectively.
• their ⁇ l, 2-xylosyltransferase activity is less than 50%, in particular less than 20%, particularly preferred 0%, of the ⁇ l, 2-xylosyltransferase activity occurring in natural plants or plant cells, respective- ly.
• the advantage of these plants or plant cells, respectively is that the glycoproteins produced by them do not comprise any or hardly comprise any ⁇ l,2-bound xylose. If products of these plants are taken up by human or vertebrate bodies, there will be no immune reaction due to the ⁇ l,2-xylose epitope.
• the invention also relates to a PNA molecule comprising a base sequence complementary to the sequence of the DNA molecule according to the invention.
• PNA peptide nucleic acid
• PNA peptide nucleic acid
• PNA generally hybridizes with complementary DNA-, RNA- or PNA-oligomers by Watson-Crick base pairing and helix formation.
• the peptide backbone ensures a greater resistance to enzymatic degradation.
• the PNA molecule thus is an improved antisense agent .
• nucleases nor proteases are capable of attacking a PNA molecule.
• the stability of the PNA molecule, if bound to a complementary sequence, comprises a sufficient steric blocking of DNA and RNA polymerases, reverse transcriptase, telomerase and ribosomes .
• the publication by Pooga et al., "Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo" (Nature Biotechnology 16:857-861; 1998) relates to PNA molecules in general and specifically to a PNA molecule that is complementary to human galanin receptor type 1 mRNA.
• the PNA molecule comprises the above-mentioned sequence, it will bind to the DNA or to a site of the DNA, respectively, which codes for ⁇ l, 2-xylosyltransferase and in this way is capable of inhibiting transcription of this enzyme. As it is neither transcribed nor translated, the PNA molecule will be prepared synthetically, e.g. by aid of the the t-Boc technique.
• a PNA molecule which comprises a base sequence which corresponds to the sequence of the inventive DNA molecule.
• This PNA molecule will complex the mRNA or a site of the mRNA of ⁇ l, 2-xylosyltransferase so that the translation of the enzyme will be inhibited. Similar arguments as set forth for the antisense RNA apply in this case.
• a particularly efficient complexing region is the translation start region or also the 5 '-non-translated regions of mRNA.
• a further aspect of the present invention relates to a method of preparing plants or plant cells, respectively, in particular plant cells which comprise a blocked expression of the ⁇ l,2-xylo- syltransferase at the transcription or translation level, respectively, which is characterized in that inventive PNA molecules are inserted in the cells .
• inventive PNA molecules are inserted in the cells .
• conventional methods such as, e.g., electroporation or microinjection, are used.
• Particularly efficient is insertion if the PNA oligomers are bound to cell penetration peptides, e.g. transportan or pAntp (Pooga et al., 1998, Nature Biotechnology, 16; 857-861).
• the invention provides a method of preparing recombinant glycoproteins which is characterized in that the inventive, recombinant plants or plant cells, respectively, whose ⁇ l, 2-xylosyl- transferase production is suppressed or completely blocked, respectively, or plants or cells, respectively, in which the PNA molecules have been inserted according to the method of the invention, are transfected with the gene that expresses the glyco- protein so that the recombinant glycoproteins are expressed.
• vectors comprising genes for the desired proteins are transfected into the host or host cells, respectively, as has also already been described above.
• the transfected plant cells will express the desired proteins, and they have no or hardly any ⁇ l,2-bound xylose. Thus, they do not trigger the immune reactions already mentioned above in the human or vertebrate body. Any proteins may be produced in these systems.
• a method of preparing recombinant human glycoproteins is provided which is characterized in that the recombinant plants or plant cells, respectively, whose ⁇ l, 2-xylosyltransferase production is suppressed or completely blocked, or plants or cells, respectively, in which PNA molecules have been inserted according to the method of the invention, are transfected with the gene that expresses the glycoprotein so that the recombinant glycoproteins are expressed.
• tissue of this plant comprise the recombinant glycoprotein so that, e.g. by extraction of the recombinant glycoprotein from the tissue and subsequent administration, or directly by eating the plant tissue, respectively, the recombinant glycoprotein is taken up in the human body.
• a method of preparing recombinant human glycoproteins for medical use wherein the inventive, recombinant plants or plant cells, respectively, whose ⁇ l, 2-xylosyl- transferase production is suppressed or completely blocked, respectively, or plants or cells, respectively, into which the PNA molecules have been inserted according to the method of the invention, are transfected with the gene that expresses the glycoprotein so that the recombinant glycoproteins are expressed.
• any protein can be used which is of medical interest.
• the present invention relates to recombinant glycoproteins according to a method described above, wherein they have been prepared in plant systems and wherein their peptide sequence comprises less than 50%, in particular less than 20%, particularly preferred 0%, of the ⁇ l,2-bound xylose residues occurring in proteins expressed in non-xylosyltransferase-reduced plant systems.
• glycoproteins which do not comprise ⁇ l,2-bound xylose residues are to be preferred.
• the amount of ⁇ l,2-bound xylose will depend on the degree of the above-described suppression of the ⁇ l, 2-xylosyltransferase.
• the invention relates to recombinant human glycoproteins which have been produced in plant systems according to a method described above and whose peptide sequence comprises less than 50%, in particular less than 20%, particularly preferred 0%, of the ⁇ l,2-bound xylose residues occurring in the proteins expressed in non-xylosyltransferase-reduced plant systems.
• a particularly preferred embodiment relates to recombinant human glycoproteins for medical use which have been prepared in plant systems according to a method described above and whose peptide sequence comprises less than 50%, in particular less than 20%, particularly preferred 0%, of the ⁇ l,2-bound xylose residues occurring in the proteins expressed in non-xylosyltransferase-reduced plant systems.
• the glycoproteins according to the invention may include other bound oligosaccharide units specific for plants, whereby - in the case of human glycoproteins - they differ from these natural glycoproteins. Nevertheless, by the glycoproteins according to the invention, a slighter immune reaction or no immune reaction at all, respectively, is triggered in the human body, since, as has already been explained in the introductory portion of the specification, the ⁇ l,2-bound xylose residues, together with ⁇ l,3-fu- cose residues, are the main cause for the immune reactions or cross immune reaction, respectively, to plant glycoproteins.
• a further aspect comprises a pharmaceutical composition comprising the glycoproteins according to the invention.
• the pharmaceutical composition comprises further additions common for such compositions.
• suitable diluting agents of various buffer contents e.g. Tris-HCl, acetate, phosphate, pH and ionic strength
• additives such as tensides and solubilizers (e.g. Tween 80, Po- lysorbate 80)
• preservatives e.g. Thimerosal, benzyl alcohol
• adjuvants e.g. ascorbic acid, sodium metabisulfi- te
• emulsifiers fillers (e.g.
• lactose, mannitol covalent bonds of polymers, such as polyethylene glycol, to the protein, incorporation of the material in particulate compositions of polymeric compounds, such as polylactic acid, polyglycolic acid, etc. or in liposomes, auxiliary agents and/or carrier substances which are suitable in the respective treatment.
• Such compositions will influence the physical condition, stability, rate of in vivo liberation and rate of in vivo excretion of the glycoproteins of the invention.
• the invention also provides a method of selecting DNA molecules which code for a ⁇ l, 2-xylosyltransferase, in a sample, wherein the labelled DNA molecules of the invention or partial sequences thereof, are added to the sample, which bind to the DNA molecules that code for a ⁇ l, 2-xylosyltransferase.
• the hybridized DNA molecules can be detected, quantitated and selected.
• the sample is denatured, e.g. by heating.
• One possible way is to separate the DNA to be assayed, possibly after the addition of endonucleases, by gel electrophoresis on an agarose gel. After having been transferred to a membrane of nitrocellulose, the labelled DNA molecules according to the invention are admixed which hybridize to the corresponding homologous DNA molecule ("Southern blotting").
• Another possible way consists in finding homologous genes from other species by PCR-dependent methods using specific and/or degenerated primers, derived from the sequence of the DNA molecule according to the invention.
• the labelled DNA molecules of the invention or partial sequences thereof are immobilized onto carrier matrices.
• DNA microarrays (“gene chips") is a further possible way to find homologous genes or to study the expression level of homologous genes.
• DNA representing either the entire genomic gene sequence, the full-length cDNA sequence, parts of these sequences or any combination of partial sequences is immobilized onto carrier matrices, in order that homologous genes, after adding the sample to the carrier matrices, hybridize with the labelled DNA molecules (for examples see e.g. Ferea T.L. & Brown, P.O., 1999, Current Opinion in Genetics & Development 9 : 715-722 and references cited herein) .
• the sample for the above-identified inventive method comprises genomic DNA of a plant organism.
• genomic DNA of a plant organism.
• a large number of plants or other species is assayed in a very rapid and efficient manner for the presence of the ⁇ l, 2-xylosyl- transferase gene.
• the invention also relates to DNA molecules which code for a ⁇ l, 2-xylosyltransferase which have been selected according to the three last-mentioned methods and subsequently have been isolated from the sample. These molecules can be used for further assays. They can be sequenced and in turn can be used as DNA probes for finding ⁇ l, 2-xylosyltransferases . These - labelled - DNA molecules will function for organisms, which are related to the organisms from which they have been isolated, more efficiently as probes than the DNA molecules of the invention.
• a further aspect of the invention relates to a preparation of ⁇ l, 2-xylosyltransferase cloned according to the invention which comprises isoforms having pi values of between 6.0 and 9.0, in particular between 7.50 and 8.00.
• the pi values of a protein is that pH value at which its net charge is zero and is dependent on the amino acid sequence, the glycosylation pattern as well as on the spatial structure of the protein.
• the ⁇ l, 2-xylosyltransferase may comprise several isoforms which have a pi value in this range.
• the reason for the various isoforms of the transferase are, e.g., different glycosylations as well as limited proteoly- sis.
• the pi value of a protein can be determined by isoelectric focussing, which is known to the skilled artisan.
• the main isoform of the enzyme has an apparent molecular weight of 60,2 kDa.
• the preparation of the invention comprises an isoform having a pi value of 7.52.
• the invention also relates to a method of preparing "plantified" carbohydrate units of human and other vertebrate glycoproteins or other glycoconjugates, wherein UDP-xylose as well as ⁇ l, 2-xylosyltransferase encoded by an above-described DNA molecule are added to a sample that comprises a carbohydrate unit or a glycoprotein, respectively, so that xylose in ⁇ l,2-position is bound by the ⁇ l, 2-xylosyltransferase to the carbohydrate unit or to the glycoprotein, respectively.
• UDP-xylose as well as ⁇ l, 2-xylosyltransferase encoded by an above-described DNA molecule are added to a sample that comprises a carbohydrate unit or a glycoprotein, respectively, so that xylose in ⁇ l,2-position is bound by the ⁇ l, 2-xylosyltransferase to the carbohydrate unit or to the glycoprotein, respectively.
• Fig. 1 shows the amino acid sequence of soybean peptide 2 and 3 (patent W099/29835; SEQ ID NO: 3 and 5), the homology between these peptides and a A. thaliana sequence as well as the DNA sequence of four primers 1-4;
• Fig. 2 shows the cDNA sequence of ⁇ l, 2-xylosyltransferase including 226 nt of the 5 ' -untranslated region
• Fig. 3 shows the amino acid sequence of ⁇ l, 2-xylosyltransferase derived therefrom
• Figs. 4a, 4b and 4c show the alignment of A. thaliana ⁇ l, 2-xylosyltransferase cDNAs, one genomic DNA and one EST sequence;
• Fig. 5 shows the alignment of amino acid sequences of ⁇ l, 2-xylosyltransferase derived from the cDNAs, from a genomic DNA and from a EST sequence;
• Fig. 6 is a schematic representation of the ⁇ l, 2-xylosyltransferase as well as the PCR-products and the hydrophobicity of the amino acid residues;
• Fig. 7 shows a comparison of the ⁇ l, 2-xylosyltransferase activity of insect cells transfected with the ⁇ l, 2-xylosyltransferase gene with that of a negative control;
• Figs. 8a and 8b shows the structure of the acceptor substrate and product of the ⁇ l, 2-xylosyltransferase
• Fig. 9 shows mass spectra
• Fig. 10 shows the analysis of the ⁇ l, 2-xylosyltransferase product by reversed-phase HPLC
• Fig. 11 shows the alignment of the predicted amino acid sequence derived from the cDNA of the present application with the amino acid sequence of the ⁇ l, 2-xylosyltransferase purified from soybean.
• Primers for the amplification of the putative ⁇ l, 2-xylosyltransferase cDNA by RT-PCR were designed as follows: A BLASTP search of the DDBJ database using two soybean peptides (SEQ ID NO: 1 and 2; corresponding to SEQ ID NO: 3 and 5 in Fig. 4 in patent W099/29835 Al; however, the C-terminal amino acids LG were omitted from SEQ ID NO: 5) (see Fig.l) showed one protein sequence derived from a Arabidopsis thaliana genomic DNA sequence (Ace. Nr. AB015479) with more than 80 % homology (SEQ ID NO: 3) .
• Primers 3 (SEQ ID NO: 4) and 4 (SEQ ID NO: 5) were based on the A. thaliana sequence homologous to the soybean peptides 2 and 3. Analysis of the homologous genomic DNA sequence using Gene-Finder at the BCM Search Launcher resulted in one predicted protein.
• Primer 1 (SEQ ID NO: 6) was designed to include the start codon of the predicted protein, whereas primer 2 (SEQ ID NO: 7) contains the stop codon of the predicted protein.
• the first strand cDNA was subjected to a PCR, wherein different combinations of sense and antisense primers were used (illustrated in Fig. 6) :
• the product of primer 3 and primer 4 was a DNA fragment with length of 174 bp (PI)
• the product of primer 1 and primer 2 was a 1605 bp (P2) DNA fragment
• the product of primer 1 and primer 4 was a DNA fragment with length of 1525 bp (P3)
• primer 3 and primer 4 produced a DNA of 254 bp (P4) .
• primer 1 and primer 2 were used for amplifi- cation of the putative open reading frame.
• a PCR reaction contained in a total volume of 50 ⁇ l 0.2 ⁇ mol of each primer, 0.05 ⁇ iM dNTPs, 2 mM MgS0 4 , 20 mM Tris- HC1 (pH 8.2 at 25°C) , 10 mM KCl, 10 mM (NH 4 ) 2 S ⁇ 4, 0.1 % Triton X- 100, 5 ⁇ g nuclease-free BSA and 2.5 units Pfu DNA polymerase from Promega.
• a first denaturing step at 94°C for 2 min, 30 cycles of 1 min at 92°C, 40 sec at 53°C and 3 min and 30 sec at 72°C were performed.
• the last extension step was carried out at 72°C for 8 min.
• PCR products were subcloned into Smal linearised and dephosphorylated pucl9 vector, and sequenced: The sequences of the subcloned fragments were obtained by means of the didesoxynu- cleotide method (ABI PRISM Dye Termination Cycle Sequencing Ready reaction Kit and ABI PRISM 310 Genetic analyzer from Perkin Elmer) . As a result of the RT-PCR three slightly different cDNA sequences were obtained. The sequence of cDNA 6 which has a size of 1605 bp (xt-Ath6; SEQ ID NO: 8) and codes for a protein of 534 amino acids having a molecular weight of 60,2 kDA and a theoretical pi value of 7,52 (see Fig.
• cDNA 9 shows 4 base pair changes compared to cDNA 6, whereas cDNA 16 shows 6 base pair changes compared to cDNA 6 (illustrated in Figs. 4a, 4b and 4c). Therefore the amino acid sequence derived from cDNA 9 comprises two changes compared to the amino acid sequence derived from cDNA 6 (SEQ ID NO: 8) , and the amino acid sequence of cDNA 16 shows four changed residues (illustrated in Fig. 5) .
• Fig. 3 shows the cDNA-derived amino acid sequence (SEQ ID NO: 9) of the ⁇ l, 2-xylosyltransferase (xt-Ath6; SEQ ID NO: 8). Potential sites for the asparagine-bound glycosylation are at Asn51, Asn301 and Asn479.
• Figs. 4a, 4b and 4c show the alignment of ⁇ l, 2-xylosyltransferase nucleotide sequences from the A. thaliana cDNA 6 (xt-Ath6; SEQ ID NO: 8), the A. thaliana cDNA 9 (xt-Ath9) , the A. thaliana cDNA 16
• the genomic sequence (xtAthEST) .
• the dotted line stands for the consensus sequence; the dashed line for a gap.
• the genomic sequence (xt-Athgen; Ace. No. AB015479, start codon at position 58185-58187, stop codon at position 60214-60216 of the genomic DNA) results from removing of two putative introns (intron 1: from position 58881 to 59116 of the genomic DNA; in- tron 2: from position 59268 to 59458 of the genomic DNA) using the splice site prediction server NetPlantGene.
• the A. thaliana EST sequence (xt-AthEST; Ace. No. AI994524) is the result of a database search using BLASTN.
• Fig. 5 shows the alignment of amino acid sequences from ⁇ l, 2-xylosyltransferase derived from A. thaliana cDNA 6 (xt-Ath6; SEQ ID NO: 9), from A. thaliana cDNA 9 (xt-Ath9), from A. thaliana cDNA 16 (xt-Athl6), from the A. thaliana genomic sequence (xt-Athgen), and derived from a A. thaliana EST sequence (xt-AthEST) .
• the dotted line stands for a consensus sequence; the dashed line stands for a gap.
• Fig. 6 the schematic predicted ⁇ l, 2-xylosyltransferase protein (top) and the derived hydrophobicity index using ProtScale, of the encoded protein (bottom) are illustrated, a positive hydrophobicity index meaning an increased hydrophobicity.
• P1-P4 the sizes of the four above-indicated PCR products (P1-P4) are shown in relationship to the cDNA.
• C coding for the postulated cytoplasmic region
• T for the postulated transmembrane region
• G for the postulated Golgi lumen catalytic region of the transferase.
• the cells were resuspended and homogenised in the following buffer (1 ml per 10 7 cells) : 100 mM MES buffer, pH 7.0, with 1 % Triton X-100, 1 mM DTT, 1 mM PMSF, 5 ⁇ g/ml Leu- peptin (Sigma) , 5 ⁇ g/ml E-64 (Serva) and incubated on ice for 30 min.
• the cell homogenates were assayed for ⁇ l, 2-xylosyltransferase activity. Negative controls were carried out with the same number of uninfected cells.
• the assay mixtures contained, in a total volume of 20 ⁇ l, 13 ⁇ l of homogenised cells, 2 nmol dabsylated GnGn hexapeptide or GnGn-pyridylamine as acceptor substrate (Fig. 8a) , 1 mM UDP-xylose as donor substrate, 10 M ATP, 20 mM MnCl2 and 1 mM 2-acetamido-l, 2-dideoxy-nojirimycin was included to prevent degradation of product by N-acetylhexosaminidase. The samples were incubated for 1 hour at 37° C and analysed by MALDI-TOF mass spectrometry.
• Fig. 7 shows the measured enzyme activity of the recombinant ⁇ l, 2-xylosyltransferase as well as of the negative control. Grey bars show the activity when GnGn hexapeptide was used as a substrate, whereas black bars indicate the use of GnGn-pyridylamin as a substrate. The enzyme activity of the cotransfected cells was 3Ox higher than that of the negative controls.
• Fig. 8a The structure of the acceptor substrate of ⁇ l, 2-xylosyltransferase is shown in Fig. 8a, and the postulated product in Fig. 8b, where R represents either a pyridylamine or dabsylated hexapeptide residue.
• Mass spectrometry was performed on a DYNAMO (BioAnalysis, Santa Fe, NM) , a MALDITOF MS which is capable of dynamic extraction (synonym for late extraction) .
• Two types of sample matrix preparations were used: dabsylated glycopeptides were dissolved in 5 % formic acid, and aliquots were applied to the target, air- dried, and covered with 1 % alpha-cyano-4-hydroxy cinnamic acid. Pyridylaminated glycans were diluted with water, applied to the target and air-dried. After addition of 2 % 2.5-dihydroxy benzoic acid, the samples were immediately dried by applying vacuum.
• Fig. 9 shows the mass spectrum of these samples, (A) being the negative control:
• the main peak (S) shows the dabsyl-Val-Gly-Glu- (GlcNAc 4 Man 3 )Asn-Arg-Thr substrate, the calculated [M+H] + value being 2262.3.
• This substrate also appears as sodium addition product and as smaller ion which has been formed by fragmentation of the Azo function of the dabsyl group, at (S*) .
• the mass spectrum (B) shows the sample with recombinant ⁇ l, 2-xylosyltransferase after incubation for 1 h at 37° C.
• the main peak (P) having a [M+H] + value of 2393.4, represents the xylosylated product .
• Xylosyltransferase assays were performed as described above under example 3 except that 10 nmol of GnGn-pyridyla ine were used as the acceptor substrate. After 4 h of incubation the sample was analyzed both by MALDI-TOF mass spectrometry and by rever sed- phase HPLC to verify the structure of the product. The presumed product peak eluting slightly ahead of the substrate GnGn-PA was collected. By MALDI-TOF MS the product's mass was determined to be 1550.9 which is in good agreement with being GnGnX-PA.
• Fig. 10 shows the analysis of the xylosyltransferase product by reversed-phase HPLC.
• A transferase incubation mixture
• B isolated xylosyltransferase product
• C isolated xylosyltransferase product after digestion with ⁇ -N-acetylglucosaminidase
• D isolated xylosyltransferase product after further digestion with alpha-mannosidase.
• the assignments of peaks are as follows: 1, GnGn-PA; 2, GnGnX-PA; 3, MMX-PA; 4, M0X-PA; 5, 00X-PAA; 6, MO-PA (from trace of substrate in isolated product) .
• N-glycan structures see Wilson I.B.H. and Altmann, F., 1998, Glycoconj. J. 15, 1055-1077.
• Fig. 11 shows the alignment of the predicted amino acid sequence according to the WO 99/29835 Al .
• This alignment shows that the amino acid sequence of the purified soybean enzym corresponds only to amino acids 199-469 of the sequence derived from the cDNA according to the present invention.
• the predicted amino acid sequence derived from the cDNA of the present application contains two insertions (corresponding to aa 375-382 and aa 425-429 of the predicted sequence) compared to the sequence of the purified soybean enzyme.

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